Journal: bioRxiv

Article Title: Determinants of metal import and specificity in a bacterial transporter

doi: 10.64898/2026.03.30.714904

Figure Lengend Snippet: (a) Schematic of our fluorescent reporter system that leverages both transcriptional and translational control to couple intracellular Mn 2+ concentration to fluorescence. (b) Example green fluorescence distributions (kernel density estimates) measured by flow cytometry for E. coli cells expressing WT DraNramp (yellow), M230A (orange), and two variants with low (N59D; teal) or no (D56A; dark gray) transport activity, alongside the pET28a empty vector (light gray). The x-axis is plotted on a logicle scale and events were gated to have similar cell sizes as measured by side scatter. (c) Dose-response curves normalized to the D56A data relating MnCl 2 concentration in the growth medium to fluorescence for the same variants as in (b), with overlaid fits to a sigmoid curve (resulting kinetic parameters listed in Supplementary Table 1). Error bars represent standard error of the mean from three replicates; sample raw distributions and an overview of the analysis are in . (d) At the bottom is a kernel density plot showing the distribution of cells in the first replicate of the evolution-guided library screen on the correlated green fluorescence (FITC-A) and side scatter area axes; approximate locations of the four sorted bins are overlaid. Above is the log-transformed enrichment of WT and two variants with intermediate (M230A) or no (D56G) Mn 2+ transport activity, highlighting how enrichment scores vary across bins for different variants. (e) Distribution of Mn 2+ activity scores for substitutions in the evolution-guided library across mutational depth. Scores range between ∼0 to ∼1 (representing no activity to WT-like levels of activity), with scores above 1 representing improved activity and scores below zero likely representing experimental noise. (f) Heatmap of Mn 2+ import scores for all variants with single mutation at positions with at least 5 measured variants, primarily from the binding-site library. White circles mark wildtype amino acids. Gray positions lack data.

Article Snippet: We transformed these ligation products into electrocompetent DH10B E. coli (GoldBio) and the requisite number of colonies were harvested from agar plates to bottleneck each subpool to ∼40X the subpool diversity to balance obtaining nearly every variant with attaining a reasonable barcode diversity.

Techniques: Control, Concentration Assay, Fluorescence, Flow Cytometry, Expressing, Activity Assay, Plasmid Preparation, Transformation Assay, Mutagenesis, Binding Assay

Journal: bioRxiv

Article Title: Determinants of metal import and specificity in a bacterial transporter

doi: 10.64898/2026.03.30.714904

Figure Lengend Snippet: (a) MgKO, a Mg 2+ -auxotrophic strain of E. coli lacking any genetically encoded Mg 2+ transporters, can only survive in low Mg 2+ when rescued with a functional Mg 2+ transporter. (b) Example growth curves in LB supplemented with 1 mM MgSO 4 with 20 µM IPTG, showing robust growth for the Mg 2+ -transporting M230A variant (orange), no growth for the non-transporting WT DraNramp (gold), and intermediate growth for two replicates of the evolution-guided library (purple and teal). (c) Growth rates, normalized to WT in 1 mM supplemental MgSO 4 , measured across concentrations of Mg 2+ supplemented into LB medium. Rates are higher for M230A (right) compared to WT (left). Error bars represent standard error of the mean across three replicates. (d) Distribution of Mg 2+ import scores from the combined libraries, colored by whether the M230 position is mutated, with the region with scores above 2 (representing clear Mg 2+ import) in an inset. (e) Growth rates of isolated clones for a selected set of variants with no M230 mutation that have Mg 2+ import scores significantly higher than WT. M230A is included as a positive control. Stars represent significance thresholds from a series of Welch’s t-tests against the WT with a Benjamini-Hochberg correction (*: p<0.05). (f) Heatmaps of Mg 2+ import scores for all mutations to TM6 on the WT (top) and M230A (bottom) backgrounds. Black circles mark wildtype amino acids. Gray positions lack data. The 230 column is identical between heatmaps. Above the heatmaps is a snapshot of TM6 (PDB ID: 8E6N). The black asterisk approximates the bound Mn 2+ ; Mg 2+ may or may not bind the same site in the M230A variant. (g) Twenty-eight variants from the evolution-guided library with scores significantly outside the distribution defined by WT barcodes (FDR < 0.05 via Student’s t-test with a Benjamini-Hochberg correction). Variants were clustered based on which residues (color-coded by chemical property) were mutated using clustermap in seaborn. Arrows above and corresponding boxed columns highlight the positions of observed sequence couplings (purple: positions 54 and 275; green: positions 232 and 381/382). The asterisk represents a deletion of residues 125-127. (h) Scatterplot of Mg 2+ import scores for all single mutations present on both the WT (horizontal axis) and M230A (vertical axis) background. The gray diagonal line represents mutations with the same overall activity level on both backgrounds, while the horizontal gray lines represent the WT score (0.00 ± 0.04) or M230A score (7.29 ± 0.62). The black curve represents a fit to a site-independent sigmoid model, demonstrating how the mutations deviate considerably from an additive model even accounting for sigmoidal global epistasis. The shaded region around the sigmoidal curve represents a 99.7% confidence interval. A selection of mutations that improve Mg 2+ on their own are highlighted in teal, and several M230 mutations (which by definition have the same effect on each background) in orange.

Article Snippet: We transformed these ligation products into electrocompetent DH10B E. coli (GoldBio) and the requisite number of colonies were harvested from agar plates to bottleneck each subpool to ∼40X the subpool diversity to balance obtaining nearly every variant with attaining a reasonable barcode diversity.

Techniques: Functional Assay, Variant Assay, Isolation, Clone Assay, Mutagenesis, Positive Control, Sequencing, Activity Assay, Selection

Journal: EMBO Reports

Article Title: SUMOylation of protein phosphatase 5 regulates phosphatase activity and substrate release

doi: 10.1038/s44319-024-00250-2

Figure Lengend Snippet: Reagents and tools table

Article Snippet: DH5-alpha Electrocompetent E coli , Goldbio , Cat# CC-203.

Techniques: Recombinant, Sequencing, Synthesized, Software, In Vitro

Journal: The Journal of Biological Chemistry

Article Title: Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii

doi: 10.1016/j.jbc.2022.102195

Figure Lengend Snippet: Identification and purification of cysteate acyl-ACP transferase. A , TLC separation of 3-keto[ 14 C]capnine (3[ 14 C]KC) arising from SulA activity using cellular lysates from Escherichia coli cells expressing nothing (empty vector control), alfi_1224 (SulA), or alfi_1465 . The thin-layer plate is representative of four independent experiments. B , purified SulA migrates as a single 85 kDa species ( V e = 76.6 ml) based on a calibrated HiLoad 16/600 Superdex 200 column (98.1 kDa theoretical homodimer mass). Left inset , molecular weight calculation using calibration standards described under . Right inset , SDS gel electrophoresis shows SulA purity (∼48 kDa) along with molecular weight standards. C , the sedimentation velocity profile (fringe displacement) was fit to a continuous sedimentation coefficient distribution model c(S). SulA sedimented as a 98.9 kDa homodimer with a sedimentation coefficient of 5.11 S. ACP, acyl carrier protein; SulA, cysteate acyl-ACP transferase.

Article Snippet: E. coli strain BL21(DE3) cells harboring the pET-SulA or pET-SulA(K281A) expression plasmids were grown in 2 l LB medium with 50 μg/ml kanamycin (Gold Biotechnology) at 37 °C and 200 rpm shaking to A 600 = 0.6.

Techniques: Purification, Activity Assay, Expressing, Plasmid Preparation, Molecular Weight, SDS-Gel, Electrophoresis, Sedimentation